GenePattern
Manage Modules & Pipelines
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version  name  owner  source 
  a
describe it here
1 0 lkplkplkp Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  a
describe it here
1 0 m.hiroki Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  a
describe it here
1 0 mariawahid Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  A
describe it here
1 0 haubinz@126.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  aa
describe it here
1 0 h-tengfei@hotmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  aalya
describe it here
1 0 acelyaavci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  AddFCSEventIndex
Adds indexes to events in a Flow Cytometry Standard (FCS) data file.
2 Added fix for parsing empty keyword values pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  AddFCSParameter
Add parameters and their values to a FCS data file
2 Added fix for parsing empty keyword values pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  AddNoiseToFCS
Add noise to specified parameters in an FCS data file.
2 Added fix for parsing empty keyword values pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Affymetrix
2 daniallmasood Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 daniallmasood Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  AffySTExpressionFileCreator
Creates a GCT file from a set of CEL files from Affymetrix ST arrays.
2 Updated to use the genepattern/affy-st-expression-file-creator:2 Docker image bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
0.14 Updated to make use of the R package installer. pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  alexs_simple_pipeline
1 atwenzel2 Installed from zip
  All.posibel.combinations.pipeline.clustering
2 mperez Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 mperez Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ALLAML
describe it here
1 0 Andyred419 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ALM
describe it here
1 0 ankstella123@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Amaretto
Discovery of driver genes using epigenomic, genomic and transcriptomic data using module networks with penalized regression.
2 Change location of data for the gene.sets.database parameter from ftp://gpftp.broadinstitute.orf to https://datasets.genepattern.org ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Change location of data for the gene.sets.database parameter from ftp://gpftp.broadinstitute.orf to https://datasets.genepattern.org ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
0.53 Initial Revision ted Installed from zip
0.46 Working revision from Gevaert lab git repo on 10/16/18 ted Installed from zip
0.42 Working revision from Gevaert lab git repo on 10/16/18 ted Installed from zip
  AmpliconSuite
A multithread-enabled quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. PrepareAA supports hg19 (or GRCh37), hg38 as well as mouse genome mm10 (or GRCm38). PrepareAA can also be invoked to start at intermediate stages of the data preparation process. <br> All credits go to: https://github.com/jluebeck/PrepareAA <br> View licenses here: <a href="https://github.com/genepattern/AmpliconSuite#licenses">https://github.com/genepattern/AmpliconSuite#licenses</a> <br/> <p> To increase your GenePattern disk space quote so you can more easily upload the input bam files, <b><a href="https://forms.gle/23tkh98vwkhtCeKM7">click here to join the AmpliconSuiteUsers group on this server.</b> </a> </p> To run multiple samples at once, simply drag and drop multiple samples into the input options. There is no need to check the "Batch" box. <br> Currently using Amplicon Architect version 1.3.4.
41 updated parameters & dockerfile edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
40 updated parameters & dockerfile edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
39 updated parameters & dockerfile edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
38 updated parameters & dockerfile edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
37 updated parameters & dockerfile edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
35 updated parameters & dockerfile edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
34 new ECDNA tag edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
33 New docker image for environment, updates to documentation for running Batch mode, updates to parameter description. edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
31 New Docker image, with new arguments. edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
28 New Docker image, with new arguments. ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  AmpliconSuiteAggregator
Aggregates individual AmpliconSuite runs. Takes in zip files (or .tar.gz) and aggregates the results. Results can directly be used to load onto AmpliconRepository.
11 added license acceptance & new ecdna tag edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10 added license acceptance & new ecdna tag edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
7 New post method for Aggregator and API. edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
6 New post method for Aggregator and API. edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
5 New post method for Aggregator and API. edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4 New docker, new arguments, new features for aggregator edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Added new parameter for AmpRepo support, Amp classifier support ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  analisiDatiRNAseq
1 isaia Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Analysis.of.Affymetrix.Microarray.Data
2 ps1277 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 ps1277 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Analyzing.microarray.data.CEL.and..clm
3 Chris96 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 Chris96 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Chris96 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Anlise.CEL
describe it here
1 0 iael.minu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ARACNE
Runs the ARACNE algorithm for reverse engineering cellular networks
2 fix problem with processing transcription factor list parameter pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  AreaChange
Calculates fraction of area under the spectrum that is attributable to signal (area after noise removal / original area)
2 Updated for R 2.5.0 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ArrayAnalysis_1.0
describe it here
1 0 jason.a.horton Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  asdf
describe it here
1 0 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  aSf
describe it here
1 0 babakke Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  AuDIT
Automated Detection of Inaccurate and Imprecise Transitions in MRM Mass Spectrometry
9 Dockerized for cloud ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
8 Dockerized for cloud ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  bat
describe it here
1 0 ayende1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  batch.effect
describe it here
1 0 jayakumarvn Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  bb
1 marygold Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  BedToGtf
Converts BED files to GFF or GTF format
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Beroukhim.Getz.2007.PNAS.Glioma.GISTIC
2 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Beroukhim.Getz.2007.PNAS.Glioma.GISTIC2.0
4 edwin5588 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 edwin5588 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 edwin5588 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 edwin5588 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Bhagwat
1 bhagwat.jadhav6001@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  BHIL_TEST_MiniReg
describe it here
2 0 bhill@broadinstitute.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 bhill@broadinstitute.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  biobaza.GSEA
4 kacper_maciejewski Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 kacper_maciejewski Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 kacper_maciejewski Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 kacper_maciejewski Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Biotech_MUL_ex4
Pipeline for Exercise 4 @ Biotechnology Masters Biostatistics Course
1 v.0.1 botomj@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  BiotechMUL_ex4_preprocessing
Data preprocessing pipeline for GSE635
1 The first working version. jj.chrzanowski1 Installed from zip
1 The first working version. jedrzej.chrzanowski Installed from zip
  blah
describe it here
1 0 hb739 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  BobbiesTESTFilter
1 bhill@broadinstitute.org Installed from zip
  borr
2 marygold Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 marygold Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  bowtie.alignment
describe it here
7 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  bowtie.alignment
describe it here
4 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  bra
describe it here
2 0 Busra Nur Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Busra Nur Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  bulk.RNAseq
describe it here
1 0 lclubb Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  BWA.aln
A fast and accurate short-read alignment tool that allows for mismatches and gaps. Alignments are output in a SAM format file, which provides Phred-scale quality scores for each alignment. Uses BWA 0.7.4 aln and samse/sampe.
2.1 Updated BWA.Index drop down menu to new BWA module support files location at datasets.genepattern.org (Amazon S3). and specify docker image, to production edwin5588 A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1.20 Updated BWA.Index drop down menu to new BWA module support files location at datasets.genepattern.org (Amazon S3). and specify docker image edwin5588 A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1.19 Updated to BWA 0.7.4, changed to use dynamic FTP-hosted index files, and switched to HTML-based doc pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  BWA.bwasw
Aligns long sequences (>200 bp) to a sequence database using BWA 0.7.4 bwasw.
1.17 Update BWA.index to new index location (datasets.genepattern.org) and update dockerfile, to production edwin5588 A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1.16 Update BWA.index to new index location (datasets.genepattern.org) and update dockerfile edwin5588 A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1.14 Updated to BWA 0.7.4, changed to use dynamic FTP-hosted index files, and switched to HTML-based doc pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  BWA.indexer
Creates a BWT index from a sequence FASTA file
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.10 updated dockerfile and commandline to run script at dockerfile location, to production edwin5588 A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1.9 updated dockerfile and commandline to run script at dockerfile location edwin5588 A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1.8 Updated to BWA 0.7.4 and switched to HTML-based doc pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  CART
Classification and Regression Tree
2 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  CARTXValidation
Classification and Regression Tree X-Validation
2 Updated for R 2.5.0 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.2 Added html doc and outputs classification results for each iteration pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  CCA_paired.T.test
8 cho Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
7 cho Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 cho Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 cho Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 cho Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 cho Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 cho Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 cho Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CCLE.geneset
describe it here
1 0 gopalp Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  cd8
describe it here
1 0 AlessioRicci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CellFie
CellFie: Cellular Functions InferencE - An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks. Please refer to the documentation for details about the procedure.
5 update to reaction models bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  check.disk.size
just does a df -sh .
3 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  chr20
describe it here
1 0 SGY Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  chris.pipeline
describe it here
1 0 yesimtutuncu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Ciao
4 mauro campanella Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 mauro campanella Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 mauro campanella Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 mauro campanella Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ClassNeighbors
Select genes that most closely resemble a profile
1 Added email address to owner contact pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  cloud_miniregression_pipeline
Test pipeline
1 initial one edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  cls.file.generator
2 guest_96371 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 guest_96371 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ClsFileCreator
A tool to create a class label (CLS) file.
4 JavaScript implementation pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4.1 S3 file fix tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3.16 Fixed bug with parsing gct files with Windows line endings pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  cluster
describe it here
1 0 polenkom Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  cluster
describe it here
1 0 yanwang Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Cluster.of.cluster
2 wyatkn Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 wyatkn Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Cluster0_ssGSEA
5 jbaronas Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 jbaronas Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 jbaronas Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 jbaronas Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 jbaronas Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Clustered.heat.map
7 314159 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Clutering.hierarchical.pipeline
1 mperez Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  cms
describe it here
1 0 cherlynty Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CN.Analysis
describe it here
1 0 parsas@mskcc.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CNToXCN
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  CNV
describe it here
1 0 huangzr Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  cnv.analysis
describe it here
2 0 Washaakh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Washaakh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CNV.Analysis
describe it here
1 0 Washaakh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CNV1
1 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  cnv_luad
1 xiejinye Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  coad
describe it here
1 0 michaela1688 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CoGAPS
Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.
0.93 set quality to 'development', set categories='Tutorial' ted Installed from zip
0.9 set quality to 'development', set categories='Tutorial' ted Installed from zip
0.8 set quality to 'development', set categories='Tutorial' ted Installed from zip
0.6 set quality to 'development', set categories='Tutorial' ted Installed from zip
0.6.9 set quality to 'development', set categories='Tutorial' ted Installed from zip
0.5 set quality to 'development', set categories='Tutorial' ted Installed from zip
0.2 set quality to 'development', set categories='Tutorial' ted Installed from zip
0.1 set quality to 'development', set categories='Tutorial' ted-dev Installed from zip
0.1.9 set quality to 'development', set categories='Tutorial' ted Installed from zip
  CollapseDataset
Collapses expression values from multiple input ids that map to a single target gene to a single value on a per-sample basis
2.2.0 10/03/2022 : Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.1.5 09/15/2022 : Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.1.4 03/02/2022 : Removed Log4J entirely from the code base. Fixed weighted_p1.5 computation. Added min dataset size warnings. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  CollapseDataset
describe it here
1 0 monser9610 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ComBat
Batch Correction - Not intended for use with single-cell RNA-seq data.
3.6 new batch correction tag edwin5588 Installed from zip
3.1 Setting parameter create.prior.plots to only receive no as an accepted value. Temporary patch. edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Combat.Pipeline
11 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
10 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
9 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
8 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
7 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 kpagacz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ComBat_Seq
ComBat_Seq module. A Batch effect adjustment tool for bulk RNA-seq count data. Improvement upon ComBat, and uses a negative binomial regression to model batch effects. ComBat-seq takes untransformed, raw count matrix as input. Provides adjusted data which preserves the integer nature of counts, so that the adjusted data are compatible with the assumptions of state-of-the-art differential expression software (e.g. edgeR, DESeq2, which request untransformed count data) Original Documentation: https://github.com/zhangyuqing/ComBat-seq Credits go to Zhang et al, https://doi.org/10.1093/nargab/lqaa078
6 New base docker image (R4.2.2), updates to gct file writing to ensure description and name are at the front. edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
6.1 Added batch correction tag edwin5588 A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
5 Added new parameter (users can now select output file format), new docker image to go with it edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Update parameters, dockerfile, and script to allow more input options. edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Finished module interface, new documentations edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  comp
describe it here
1 0 GPjana Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Comparative_Marker_Retrieval_and_Analysis
3 alow Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 alow Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 alow Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ComparativeMarkerSelection
Identify differentially expressed genes that can discriminate between distinct classes of samples.
11 Updated to run in its own R 2.5 container - allowing q values to be computed. bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4 Added Paired T-Test pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ComparativeMarkerSelection_Pipeline
1 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CompareSpectra
Compares two spectra to determine similarity
3 Fixed parsing of input files, changed default value of output file, and suppressed package startup messages pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Comparison
14 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
13 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
12 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
11 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
10 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
9 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
8 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
7 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Comparison.1
describe it here
1 0 tirsa.vanwestering@ugent.vib.be Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  compmarkersel
ID diff expressed genes
4 robynm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 robynm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 robynm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 robynm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ConcatenateFilelist
Concatenate all of the items in the input filelist into a single large file.
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ConClu_12112018
1 lydia.lam Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ConCluTCGA_12112018
1 lydia.lam Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Conos.Cluster
GenePattern Module which implements the clustering and embedding steps of Conos
3 Test Docker image v3 - version control for pkgs ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.2 Test Docker image v3 - version control for pkgs edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.1 Initial version edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  Conos.Preprocess
GenePattern Module which implements the preprocessing and PCA steps of Conos
3 updated accepted file formats for input file ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.2 Test Docker image v3 - version control for pkgs edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.1 Initial version edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  Conos.VisualizeGeneExpression
This is a minimalistic implementation of visualization options for Conos. This module is intended to be used after <a href="https://cloud.genepattern.org/gp/pages/index.jsf?lsid=urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00410:0.1">Conos.Cluster</a> has been ran.
8 Initial version acastanza A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
7 Initial version acastanza A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
5 Initial version ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  consensus
describe it here
1 0 monser9610 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  consensus.clusterin.kmax.15
describe it here
1 0 monser9610 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ConsensusCluster.12318
5 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3.1 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ConsensusCluster_12112018
1 lydia.lam Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ConsensusClustering
Resampling-based clustering method
7 Fixed bugs in classpath (changed Jama-1.0.1.jar to Jama-1.0.2.jar and acme.jar to Acme.jar) pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
7.2 Updated command line to use <run-with-env> wrapper script pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  ConsensusClusterSKCM
3 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ConstellationMap
A downstream visualization and analysis tool for gene set enrichment results with interactive web visualizer.
1.4.20 Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.19 Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.18 Updated to MSigDB v7.5.1. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.17 Updated to MSigDB v7.5. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.16 Fixed minor typo. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.15 More flexible CLS parsing. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.14 Updated for MSigDB v7.4. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.13 Updated for MSigDB v7.3. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.12 Updated to MSigDB v7.2. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.11 Updated to MSigDB v7.1 eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.10 Updated to MSigDB v7.0 eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4.9 Updated to MSigDB v6.2, removed Java dependencies, portability improvements. eby@broadinstitute.org A GenePattern module repository whose content is contributed by members of the GenePattern community. These modules are not curated by the GenePattern team. GParc (GenePattern Archive)
1.4.6 Updated to MSigDB v6.1 (open-access), removed Java dependencies, portability improvements. eby@broadinstitute.org A GenePattern module repository whose content is contributed by members of the GenePattern community. These modules are not curated by the GenePattern team. GParc (GenePattern Archive)
1.4.4 Completed r.package.info edits for awsbatch and rhel6 environments pcarr@broadinstitute.org Installed from zip
1.4.2 Added Hmisc_3.12-2 dependency to 'r.package.info' pcarr@broadinstitute.org Installed from zip
1.2 Initial production release. pcarr@broadinstitute.org A GenePattern module repository whose content is contributed by members of the GenePattern community. These modules are not curated by the GenePattern team. GParc (GenePattern Archive)
  Convert.Alevin
Read alevin output files and convert them to anndata (.h5ad) or loom (.loom) format for downstream analysis. Designed to convert Alevin Velocity quantification into a compatible format for scVelo.
1 Initial Release bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Convert.gmt.to.txt
1 beltranmm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  convertcel
1 mwfoster Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ConvertLineEndings
Converts line endings to the host operating system's format.
2 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ConvertToMAGEML
Converts a gct, res, or odf dataset file to a MAGE-ML file
2 Fixes bug in the order of the BioDataCube pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ConvertToMAGETAB
A module to export data from GenePattern in MAGE-TAB format
2 Added types for text parameters pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  cool
describe it here
1 0 Mrohr2016 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CopyNumberDivideByNormals
Determines the copy number of a target SNP
3 Updated to accept Allele-specific SNP files. pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  CopyNumberFromArray
ZH.Liu
1 wolfson Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfComparativeMarkerSelectionViewer
Views the results from ComparativeMarkerSelection
1 Bug fix to support S3 files edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfCopyNumberFromArray
ZH.Liu
1 wolfson Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfDESeq2
A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor
1 Changed to produce a GCT with the normalized counts table. Added a docker image declaration. acastanza Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfDiagnosticPipeline
1 atwenzel2 Installed from zip
1 ted Installed from zip
  copyOfGolub.Slonim.1999.Nature.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
1 Modified call to GeneListSignificanceViewer to specify Gene List input file type mmrtest-inf Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfGolub.Slonim.1999.Nature.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
1 1.0 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfGSEA
Gene Set Enrichment Analysis. <strong>If you are using GSEA on RNA-seq data, please read <a href="http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA" target="_blank">these guidelines</a>.</strong>
1 10/03/2022 : Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm. ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfHCA_exploratory_pipeline
1 edwin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfMetageneProjection
Projects one or more data sets onto the metagene representation of another data set
1 acastanza Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfMultiple_ssGSEA_ROC
Simple_ssGSEA_ROC
7 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfTCGA.SampleSelection
Retrieve TCGA data from Broad FireBrowse and perform sample selection on the basis of expression levels for specific genes of interest for analysis using GSEA tools.
1 Update for non-float MSigDB version numbers acastanza Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfUntitledPipeline3345
1 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  copyOfUntitledPipeline6041
1 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CoxRegression
Cox regression using clinical data and .cls file
3 Modified the input.cls.filename parameter to be optional ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Modified the input.cls.filename parameter to be optional ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.3 Modified the input.cls.filename parameter to be optional pcarr@broadinstitute.org Installed from zip
  CRC_practica.2
describe it here
1 0 vadrian Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CreateSymlinks
Creates symlinks to the input files in the job results directory. This is intended to be a helper module for creating scatter-gather pipelines. Note that this module is not supported on Windows
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  CsvToFcs
Converts a Comma separated values (CSV) file to a Flow Cytometry Standard (FCS) file.
2 Fix for parsing empty keyword values pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  CT60
describe it here
1 0 supreetagarwal@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CummeRbund.GeneSetReport
[Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots based on a user-provided list of genes.
0.21 Updated to make use of the R package installer. pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  CummeRbund.QcReport
[Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots and tables related to QC and Global Stats.
0.30 Updated to make use of the R package installer. pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  CummeRbund.SelectedConditionsReport
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots based on a user-provided list of conditions.
0.11 Updated to make use of the R package installer. pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  CummeRbund.SelectedGeneReport
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots based on a single user-specified gene.
0.17 Updated to make use of the R package installer. pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  CytoHiearchy.
1 Devansh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  CytoscapeViewer
Visualizes a gene network
2 Updated to Cytoscape 2.5.2 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  D5.vs.iT2
describe it here
1 0 jwang Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  dapple
describe it here
1 0 wpongster8 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DAPPLE
DAPPLE (Disease Association Protein-Protein Link Evaluator) looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature.
0.19 Official GParc release bhill@broadinstitute.org Installed from zip
  Daryl.Griffin
describe it here
1 0 darylgriffin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Data_Analysis
describe it here
1 0 Khushbakht Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DBHeatMapfromGEO
5 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 boucherd Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DE.viewer.
describe it here
1 0 aakanksha1990 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DeIdentifyFCS
DeIdentifyFCS an FCS data file; remove keywords from a list or matching a regular expression; useful to anonymize FCS data files and/or to remove specific (e.g., clinical) information
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  delete_copyOfGISTIC_2.0
Genomic Identification of Significant Targets in Cancer (version 2.0.23)
1 set job.docker.image back to 'genepattern/docker-gistic:0.13' ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  delete_me
describe it here
1 0 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DESeq2
A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor
3 Updated Dockerfile to using R 4.3, updated Deseq2 version as well. edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Changed to produce a GCT with the normalized counts table. Added a docker image declaration. ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Changed to produce a GCT with the normalized counts table. Added a docker image declaration. eby@broadinstitute.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DESeq2.Normalize
A modified version of DESeq2 to perform normalization of RNA-Seq count data without needing to perform differential expression analysis based on the DESeq2 package from Bioconductor
2.1 edjuaro Installed from zip
  DESeq2_test
2 sharonov@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 sharonov@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DESeq2_test2
3 sharonov@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 sharonov@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 sharonov@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DiagnosticPipeline
4 ted Installed from zip
  DiagnosticPipeline
3 bkellman Installed from zip
2 bkellman Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2.1 bkellman Installed from zip
2.0.1 bkellman Installed from zip
1 0.1 bkellman Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DietSeurat.QC
Seurat quality control (First step in the Seurat Suite), using Seurat version 4.0.3.
1 Reading new version of HCA (Loom), fixing the url reading bug (added a new parameter) jonzamora Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  diff
describe it here
1 0 AnnaCardusFigueras Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  diff_expression
describe it here
2 0 HUANGSHUAI Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 HUANGSHUAI Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Differential.expression.Parental
describe it here
1 0 jayakumar.vadakekolathu2@ntu.ac.uk Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DifferentialExpressionViewer
Views differential expression results such as from the ComparativeMarkerSelection module. Formerly known as ComparativeMarkerSelectionViewer.
10 Renamed from ComparativeMarkerSelectionViewer bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  DiSCoVER
Beta implementation of the DiSCoVER algorithm.
1 Displaying the control options as one drop-down menu. edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.1 Showing only upload option for contol. edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.4 Initial version + fixed an issue with the input format + adding verbosity as an option. edjuaro Installed from zip
0.2 Initial version + fixed an issue with the input format. edjuaro Installed from zip
0.1 Initial version edjuaro Installed from zip
  DiseasedHealthy.Mouse.Saliva.
describe it here
3 acelyaavci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 acelyaavci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 acelyaavci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DLBCL
describe it here
1 0 parsas@mskcc.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  dna
describe it here
1 0 Winston Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DOWNINGwwo
describe it here
1 0 dshin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  download
describe it here
1 0 guest_101923 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DownloadURL
Downloads a file from a URL
1 Added email address to owner contact pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  duh
describe it here
1 0 Diamond Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  DW_training
training
1 dwang326 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  eadj
1 alberto.peloso2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  early_versus_primary
describe it here
1 0 mschue Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  echo
echo test
5 ted Installed from zip
  echo_userdir
testuserdir
1 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  edwinharm
Harmony is a batch correction tool. Upon use, this module will produce three scatterplots. One plot will show the data pre-Harmony, and can be found in the 'BeforeHarmonyPlot.png' file. In this plot, the x and y axes represent the 1st and 2nd principal components from PCA dimensional reduction (unless specified otherwise by the user). Another plot will show the data post-Harmony, and can be found in the 'AfterHarmonyPlot.png' file. In this plot, the x and y axes the same dimensions used in the pre-Harmony plot are shown, but adjusted by Harmony. Lastly, the third plot shows the pre-Harmony and post-Harmony plots side by side for comparison.
1 Added batch correction tag edwin5588 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  EGF.WT.
describe it here
1 0 jvannostrand Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  eleonora
1 vercesie Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  EMT
describe it here
1 0 Hazafa Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Esercitazione
5 Giuseppe.serio01 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 Giuseppe.serio01 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 Giuseppe.serio01 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 Giuseppe.serio01 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Giuseppe.serio01 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  esercitazione3
1 carolina.bo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  esercitazione_magni
1 carolina94 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Esercitazione_MattiaChiesa
2 MiriamA Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 MiriamA Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Esercitazione_MattiaChiesa
1 MiriamA Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  EsercitazioneChiesa
1 MiriamA Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  EsercitazioneNGS
1 MiriamA Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ESPPredictor
Determine which tryptic peptides will generate the highest signal in ESI-MS
4 Dockerized release bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  esrcitazione
2 carolina94 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 carolina94 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ESub
1 alberto.peloso Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  esub
1 alberto.peloso2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  esub2
1 alberto.peloso2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ex1
describe it here
1 0 TasneemArsiwala Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Ex4_preprocessing
Pipeline for GenePattern based preprocessing of GSE635 data.
1.7 v.0.4 jj.chrzanowski1 Installed from zip
1.7 v.0.4 botomj@gmail.com Installed from zip
1.7 v.0.4 botomj Installed from zip
1.7 v.0.4 jedrzej.chrzanowski Installed from zip
1.6 v.0.3 jedrzej.chrzanowski Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1.5 v.0.3 jj.chrzanowski1 Installed from zip
1.5 v.0.3 jedrzej.chrzanowski Installed from zip
1.4 v.0.2 jedrzej.chrzanowski Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1.3 v.0.1 jedrzej.chrzanowski Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Example
Example1
1 GuadalupeAntonio Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Example_for_PTSP
describe it here
1 0 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  example_mutsig
2 ab12kim Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 ab12kim Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  explore
describe it here
1 0 mital14 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ExpressionFileCreator
Creates a RES or GCT file from a set of Affymetrix CEL files. For IVT arrays only; use AffySTExpressionFileCreator for ST arrays.
12.5 include R packages in container and fix for stderr output of install.packages(<repos_cdf>) pcarr@broadinstitute.org https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
12.4.1 installed R packages in container, job.docker.image='genepattern/expressionfilecreator:v12.4.1' pcarr@broadinstitute.org Installed from zip
12.3 Updated to make use of the R package installer. Fixes a bug in failing to remove downloaded annotation files. pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  ExprToGct
Converts an EXPR file to GCT format
2 Fixed handling of different newline characters pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ExtractColumnNames
Lists the sample descriptors from a .res file.
2 Annotated for GP 1.4 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ExtractComparativeMarkerResults
Creates a derived dataset and feature list file from the results of ComparativeMarkerSelection
4 Renamed field parameter to statistic pcarr@broadinstitute.org Installed from zip
2 Adds ability to extract top features by score pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  extractcompmarker
describe it here
2 0 robynm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 robynm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ExtractFCSDataset
Extract one or more FCS datasets from an FCS data file
2 Updated to include more lenient CFCS library pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ExtractFCSKeywords
Extracts keyword(s) value(s) from a Flow Cytometry Standard (FCS) file.
2 Updated to release candidate from Josef which includes more lenient CFCS library pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ExtractFCSParameters
Extract specified parameters (dimensions) from an FCS data file.
2 Fix for parsing empty keyword values pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ExtractRowNames
Extracts the row names from a .res, .gct, or .odf file.
3 Added support for gct and odf files pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  EYE.GCT
describe it here
1 0 libai Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  FastQC
Provides quality control metrics on raw sequence data
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
0.5 pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  FastqToBAM
1 joller Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  FCS.to.Cell.matrix
1 pmcerlean1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  FCS_Version_Conversion
Converts FCS files to CSV and back to allow programs to read FCS files from FACSDiVa
1 AbidingProduce Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  FCS_Version_Correction
Converts FCS files to CSV and back to FCS to allow programs to utilize unsupported FCS versions.
1 AbidingProduce Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  FcsToCsv
Converts a Flow Cytometry Standard (FCS) file to a Comma Separated Values (CSV) file.
3 Added fix for parsing empty keyword values pcarr@broadinstitute.org A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  FeatureSummaryViewer
Feature Summary Viewer
4 Updated GeneCruiser library pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 includes an interactive histogram of the features included in each cross validation run and includes interactive annotation of Affy probe IDs using GeneCruiser. pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ff
describe it here
1 0 firoz Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  fff
describe it here
2 0 xjyang1974 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 xjyang1974 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  File1_SeqCounts
describe it here
1 0 arichi Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  FileSplitter
Splits a file into equal-sized chunks, given the number of lines per output file
2 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  FilterFilelist
a helper module which generates a filtered filelist from the input filelist and some filter parameters.
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  First.try
describe it here
1 0 darshininambiar@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  First.try.012223
describe it here
1 0 21chuck Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  FLAMEPreprocess
Performs preprocessing of .fcs or .txt flow cytometric data files
4.2 Pin common.R to the one associated with v. 4 release of this module pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  focais.
describe it here
1 0 Elisabete Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  foofoo
describe it here
1 0 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  FP_HC2978
1 jbzhang Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Fpkm_trackingToGct
Takes a Cufflinks FPKM_tracking file and converts it to GCT format.
5 Updated to output scientific values and 0s as output by Cufflinks pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  FPKMUQ1500_12042018
1 lydia.lam Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  g
describe it here
1 0 HUANGSHUAI Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GBM_htseq_count
describe it here
1 0 Saleem Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  gct
describe it here
1 0 CHOIHEEJUNG Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  gct.file
describe it here
1 0 16tcv Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GctToPcl
Convert .gct to .pcl
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  GDS6083
describe it here
1 0 fzgabo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  gene.analysis
describe it here
1 0 MoeezAhmed Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  gene_expression
1 alison_lee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GeneListAll
5 yiwenh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 yiwenh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 yiwenh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 yiwenh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 yiwenh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GeneListSignificanceViewer
Views the results of marker analysis
4 Updated GeneCruiser library pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 includes interactive plots and annotation of Affymetrix probe identifiers pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  GeneNeighbors
Select genes that most closely resemble a continuous profile (e.g., another gene)
4 updated thresholds to post-2002 Affy Values pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  geneSelect_12042018
1 lydia.lam Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  genetic
describe it here
1 0 Winston Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Genomespace
describe it here
1 0 BrunoLarrivee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GEOImporter
Imports data from the Gene Expression Omnibus (GEO)
6 Updated NCIBI FTP paths. Added ability to omit rows with all NA values. Updated to use R 4.0.3 via module specific Docker container. bhill@broadinstitute.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GFP.exo.1.file.1.R1
describe it here
1 0 thepreztonlee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GFP_exo_1_S24_L001_R1_001.fastq
describe it here
1 0 thepreztonlee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  gg
describe it here
1 0 yungminc12 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  gistic
2 tothr Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 tothr Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GISTIC.1
1 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  gistic2
1 dyy Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GISTIC2_lymph_hisens_adjusted
2 dutian Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 dutian Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GISTIC_2.0
Genomic Identification of Significant Targets in Cancer (version 2.0.23)
6.15.30 Fixed remove.X tabor Installed from zip
6.15.28 Fixing Docker container tabor Installed from zip
6.15.21 added the rest of the v6.14 hard-coded args back to the command line pcarr-dev Installed from zip
6.15.20 add '-genepattern 1' back to the command line pcarr-dev Installed from zip
6.15.19 updated command line args to match the 2.0.23 example pcarr-dev Installed from zip
6.15.18 updated command line args to match the 2.0.23 example pcarr-dev Installed from zip
6.15.17 updated command line args to match the 2.0.23 example pcarr-dev Installed from zip
6.15.16 set prefix_when_specified for 'remove.X', removed default value pcarr-dev Installed from zip
6.15.15 removed '-savedata 0' command line arg pcarr-dev Installed from zip
6.15.11 refactor, commandLine format in manifest file pcarr-dev Installed from zip
6.15.10 make 'output.prefix' an optional parameter pcarr-dev Installed from zip
6.15.9 set job.docker.image to 'genepattern/docker-gistic:0.13' pcarr-dev Installed from zip
6.15.8 commandLine=gp_gistic2_from_seg ..., 'genepattern/docker-gistic:latest' pcarr@broadinstitute.org Installed from zip
6.15.7 commandLine=runMatlab.sh gp_gistic2_from_seg ..., runMatlab.sh initializes the environment in the container pcarr@broadinstitute.org Installed from zip
6.15.4 Containerized GISTIC v2.0.23, set job.docker.image='genepattern/docker-gistic:0.11, gp_gistic2_from_seg cmd in libdir' pcarr@broadinstitute.org Installed from zip
6.14 Updated to GISTIC v2.0.23, added '-maxspace' and '-logdat' params, no longer requires a markers file bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  GISTIC_2.0_default.TCGA
3 vlkjvlkj Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 vlkjvlkj Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 vlkjvlkj Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GISTIC_2defaultTCGA
2 vlkjvlkj Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 vlkjvlkj Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GISTIC_Canfam
1 hhyunji1027@naver.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GISTIC_ESCC
2 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GISTIC_test_1
4 justin28969 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 justin28969 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 justin28969 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 justin28969 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GlobalAlignment
standard global sequence analysis
0 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Golub.Slonim.1999.Nature.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
3 ted Installed from zip
2 Modified call to GeneListSignificanceViewer to specify Gene List input file type pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Golub.Slonim.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
1 Modified call to GeneListSignificanceViewer to specify Gene List input file type mmrtest5 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GR.resting
describe it here
1 0 zhliusalk Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  gse
1 inaselsayed Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSE273726_naivevmemory_genep
1 guest_100489 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSE273726_naivevmemory_genep
1 guest_100489 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSE273726_naivevmemory_genep
1 guest_100489 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSEA
Gene Set Enrichment Analysis. <strong>If you are using GSEA on RNA-seq data, please read <a href="http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA" target="_blank">these guidelines</a>.</strong>
20.4.0 10/03/2022 : Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
20.3.6 09/15/2022 : Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
20.3.5 03/02/2022 : Removed Log4J entirely from the code base. Fixed weighted_p1.5 computation. Added min dataset size warnings. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  gsea.jurkat
describe it here
1 0 marsluo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSEA.KRAS
1 okondrashova Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSEA.pipe
10 maya3 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
9 maya3 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
9.1 maya3 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
8 maya3 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
7 maya3 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 maya3 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSEA_Norm
describe it here
6 0 liuh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 0 liuh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 0 liuh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSEA_rnk
1 rluchtel Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  gsea_tex
describe it here
1 0 pjuszczynski@ihit.waw.pl Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSEA_Unt_Il22KO_v_WT
describe it here
1 0 omershomrat Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSEALeadingEdge
1 BWilde@mednet.ucla.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSEALeadingEdge2
1 BWilde@mednet.ucla.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSEALeadingEdgeViewer
Leading Edge Viewer for GSEA results
6 Updated to the GSEA 4.2.3 code base, removing Log4J entirely from the code base. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  GSEApreranked
3 jingranhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 jingranhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 jingranhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  GSEAPreranked
Runs the gene set enrichment analysis against a user-supplied ranked list of genes.
7.4.0 10/03/2022 : Fixed a manifest typo. Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
7.3.7 09/26/2022 : Fixed a manifest typo. Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
7.3.5 03/02/2022 : Removed Log4J entirely from the code base. Fixed weighted_p1.5 computation. Added min dataset size warnings. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  GYG1
describe it here
1 0 cornelius Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  H.part
describe it here
1 0 jaeryunryu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Harmony
Harmony is a batch correction tool. Upon use, this module will produce three scatterplots. One plot will show the data pre-Harmony, and can be found in the 'BeforeHarmonyPlot.png' file. In this plot, the x and y axes represent the 1st and 2nd principal components from PCA dimensional reduction (unless specified otherwise by the user). Another plot will show the data post-Harmony, and can be found in the 'AfterHarmonyPlot.png' file. In this plot, the x and y axes the same dimensions used in the pre-Harmony plot are shown, but adjusted by Harmony. Lastly, the third plot shows the pre-Harmony and post-Harmony plots side by side for comparison.
6 changed default values to be blank edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Added batch correction tag edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Added animations edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.1 Added batch correction tag edwin5588 A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1 Removed dockerhub tag and reference from description edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  HC
describe it here
1 0 larissa.cassiano Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HCA_exploratory_pipeline
1 edwin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HCA_pipe2
2 edwin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 edwin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HCA_pipe2
1 edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  heat
describe it here
1 0 harris@uthscsa.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  heat.map
describe it here
2 0 16tcv Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 16tcv Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Heat.Map.
describe it here
3 eanderson34 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 eanderson34 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 eanderson34 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  heatmap
describe it here
3 0 fkipper Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 fkipper Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 fkipper Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1.1 0 fkipper Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  heatmap
describe it here
1 0 JeffLiu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  heatmap
describe it here
1 0 JeffLiu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  heatmap
describe it here
1 0 JeffLiu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HEATMAP
describe it here
1 0 ramaniganesh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Heatmap
describe it here
1 0 Ekaterina Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Heatmap
describe it here
1 0 16tcv Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Heatmap.generation
describe it here
1 0 joannahfergusson Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Heatmap.generator.
2 eanderson34 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 eanderson34 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1.2 eanderson34 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1.1 eanderson34 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HeatMapImage
Creates a heat map from a dataset
6 Fixed bug in discrete color scheme. Added gradient color scheme option. pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  HeatMapViewer
A configurable heat map viewer that provides users with several options for manipulating and visualizing array-based data
13 Updated to improve compatibility with Java 7 security updates pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
13.11 Bug fix to support S3 files tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
13.9 Initial beta release pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  HGS_CCLE_DepMap_EMT_hallmarks
1 greta.gudoityt Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HierarchicalClustering
Hierarchical Clustering
6 Updated for Java 7 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  HierarchicalClustering_image
1 gwang6@mdanderson.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HierarchicalClusteringImage
Creates an image of the dendrogram generated from HierarchicalClustering
4 removed non-functional rows to highlight parameter, removed invalid .esp output option, added genepattern/docker-java17:0.12 to manifest bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Fixed row/column size transposing pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  HierarchicalClusteringPipeline
HierarchicalClustering
2 harbison Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 harbison Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HierarchicalClusteringViewer
Views results of hierarchical clustering.
11.5 Bug fix for S3 files tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
11.3 Converted to Javascript implementation - initial beta release pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  high
30 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
29 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
28 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
27 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
26 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
25 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
24 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
23 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
22 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
21 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
20 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
19 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
18 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
17 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
16 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
15 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
14 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
13 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
12 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
11 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
10 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
9 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
8 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
7 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HISAT2.aligner
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
3 Changed index dynamic source from ftp://gpft p to the copy on https://datasets.genepattern.org ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Changed index dynamic source from ftp://gpft p to the copy on https://datasets.genepattern.org ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 bhill@broadinstitute.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1.6 Changed index dynamic source from ftp://gpft p to the copy on https://datasets.genepattern.org ted A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1.5 Updated name and doc location bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  HISAT2Indexer
Indexes one or more FASTA files for use in the HISAT2Aligner.
1 bhill@broadinstitute.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1.9 Updating module name and doc location bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  HM
describe it here
2 0 giusy.dellagatta Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 giusy.dellagatta Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HTSeq.Count
Takes alignment files in SAM/BAM format and a feature file in GTF/GFF format (usually with exon annotation), name sorts the alignment file and calculates for each sample the number of reads mapping to each feature. (HTSeq.count v0.11.2)
4 Modified to use datasets.genepattern.org instead of ftp://gpftp.broadinstitutue.org as source for default gtf files ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Beta release bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3.1 Modified to use datasets.genepattern.org instead of ftp://gpftp.broadinstitutue.org as source for default gtf files ted A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  httpsdatasets.genepattern.orgdataall_amlall_aml_train.gct.
describe it here
2 0 Naiaradaris Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Naiaradaris Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  httpsdatasets.genepattern.orgdataall_amlall_aml_train.gct.
describe it here
1 0 guest_100230 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  httpsdatasets.genepattern.orgdataall_amlall_aml_train.gct.
describe it here
1 0 guest_100230 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  httpsdatasets.genepattern.orgdataall_amlarchiveall_aml_train.res
describe it here
1 0 Sruthi S Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Hu68kHu35kAtoU95
Converts a list of Affymetrix Hu6800/Hu35KsubA probes to the corresponding Affymetrix U95Av2 probes.
1 Updated documentation pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Human_GRCh37_hg19.fasta.gz
describe it here
1 0 Nattawan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HumanData
describe it here
2 0 16tcv Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 16tcv Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  HW1
2 Longwei Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Longwei Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  hw1
3 ntduong555 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 ntduong555 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 ntduong555 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  hw2155
2 ntduong555 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 ntduong555 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ibru
describe it here
1 0 Margaret_H Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Ident_Vis_RNAseq_data
1 rmiller@med.unc.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Ignacio.y.Estefania
describe it here
1 0 fannyemg9 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Igor_clustering
1 IgorShats Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  igv.js
Launches igv.js with input file(s)
2.5 Bug fix for S3 files tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.4 Bug fix for optional locus parameter when run from notebook bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.1 Updated to igv.js v2.3.5 tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  il1
describe it here
1 0 heba ismail Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ilker
1 ilkeraltundas Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  IlluminaExpressionFileCreator
Creates a GCT file from a zip of Illumina IDAT files and an Illumina manifest file
2 Improved handling of manifests and zip files; removed required string "_Grn" in input filenames pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  IlluminaPipeline
1 mmrtest5 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Immunome
describe it here
1 0 PAGLIUS Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  improveFigure
describe it here
1 0 snharbi Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ImputeMissingValues.KNN
Imputes missing values
13 Renamed module from ImputeMissingValues.KNN to ImputeMissingValuesKNN pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Index
describe it here
1 0 seoyoungee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  IR
describe it here
1 0 wenbin-yang@northwestern.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  IRpipeline
describe it here
1 0 blb74 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Isoform.quantification
3 alekszakirov Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 alekszakirov Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 alekszakirov Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  j
describe it here
1 0 upvgenomica Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  JavaTreeView
Hierarchical clustering viewer that reads in Eisen's cdt, atr, and gtr files. A detailed description of these formats is available from http://microarray.ccgb.umn.edu/smd/html/MicroArray/help/formats.shtml
2 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  javi
describe it here
1 0 jabemo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  JM
describe it here
2 0 john.manion Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 john.manion Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Jurkat
describe it here
1 0 ccagle Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Kallisto.Indexer
Builds an index from a FASTA formatted file of target sequences for use with Kallisto.
2 add documentation, author, docker, source code repo, change visibility to public, quality level to preproduction ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 add documentation, author, docker, source code repo, change visibility to public, quality level to preproduction edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Kallisto.Quant
Runs Kallisto to perform pseudoalignment (using a human or mouse transcriptome index) and gene-level aggregation
4 dynamic drop down for kallisto, rename to Kallisto.Quant, update parameter descriptions edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Exposing all Kallisto parameters tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Added Mouse index, Release M26 (GRCm39), and updated Human index, Release 37 (GRCh38.p13), from Gencode. tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Initial version (1.0) edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
0.1 Initial version edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  kkk
describe it here
1 0 Wallax Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  kmean.cluster
describe it here
1 0 ychmax8@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  kmeans
describe it here
1 0 monser9610 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  KMeansClustering
Module that performs the K-Means Clustering algorithm
2 Fixed listing of acceptable input file formats pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  KNN
K-nearest neighbors classification
4 Set default distance measure to Euclidean pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Added ability to save prediction model pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  KNN_pipeline_cc_noncc
1 alsawao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  KNNXValidation
KNN classification with Leave-One-Out Cross-Validation
6 Set default value of distance measure to Euclidean pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  KSscore
Computes the Kolmogorov-Smirnov score for a set of genes within an ordered list.
1 Added email address to owner contact pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  l
describe it here
1 0 lbaert Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  l
describe it here
1 0 rakangxxx Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  LA38
describe it here
1 0 LameesAb Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  LandmarkMatch
A proteomics method to propogate identifed peptides across multiple MS runs
2 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  LCMmicroarray
describe it here
1 0 jxy953 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Line
describe it here
1 0 lamantiamaria@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  line1
1 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  line2
1 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ListFiles
a helper module which outputs a filelist, the list of all files in the input directory, similar to the unix 'ls' command
0.3 Updated source code to use FindCommand and FileVisitor pattern pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  liuzaoqu
describe it here
2 0 liuzaoqu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 liuzaoqu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Liya.Ding
describe it here
3 0 WilliamHou Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 WilliamHou Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 WilliamHou Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  LocatePeaks
Locates detected peaks in a spectrum.
2 Updated for R 2.5.0 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  log
describe it here
2 0 hwichova Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 hwichova Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  LogicleTransformFCS
Logicle transformation of (selected) parameters in a list mode FCS data file.
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  LogTransform
og transform a data (gct) file.
3 Initial version edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 Initial version edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Initial version edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  logTransform
asdf
2 ted Installed from zip
  LogTransformEdwinTest
Log transform a data (gct) file.
3 Initial version edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 Initial version edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Initial version edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  LOHPaired
Computes LOH for paired samples
3 Pairings based on array name instead of sample name pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  LOOCV_SurvivalSignature
Train a predictive molecular signature for time-to-event outcome with censoring by employing leave-one-out (LOO) cross-validation procedure to minimize overfitting to outlier outcome data
3 This pipeline works on R-2.5 S226953 Installed from zip
  Look
describe it here
2 0 lamantiamaria@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 lamantiamaria@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Lu.Getz.Miska.Nature.June.2005.mouse.lung.pipeline
Normal/tumor classifier and kNN prediction of mouse lung samples
1 Updated for R 2.5 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Lu.Getz.Miska.Nature.June.2005.mouse.lung.pipeline2.0
Normal/tumor classifier and kNN prediction of mouse lung samples
1 Updated for R 2.5 edwin5588 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  LUNAR
3 jpatrico Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 jpatrico Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 jpatrico Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  LUNAR_BINARY
2 jpatrico Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 jpatrico Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  LUSC
describe it here
1 0 ThanhNguyen Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  LUSC
describe it here
1 0 ThanhNguyen Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  M1_cluster
1 isabellestaco Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  M2_cluster
1 isabellestaco Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  M39715
1 spack Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  macro
1 apaoli Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MAGEMLImportViewer
A visualizer to import data in MAGE-ML format into GenePattern
2 Fixes bug in determining if input file is in gzip format pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  MAGETABImportViewer
A visualizer to import data in MAGE-TAB format into GenePattern
2 Fixed bug with merging multiple data matrix files and also modified input parameters. pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  MakeHierarchicalClusterAndImage
1 alow Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MapChipFeaturesGeneral
Change (map) the features (genes) of a dataset
3 Fixed a broken script reference pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Mayo.MI
describe it here
1 0 tcimato Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  mbg2
1 RdvnAyaz Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  mbg421
1 RdvnAyaz Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MedGen
4 lisaschneider0509 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 lisaschneider0509 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 lisaschneider0509 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 lisaschneider0509 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MedGen
6 medgen Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 medgen Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 medgen Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 medgen Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 medgen Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 medgen Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MedGen1
2 lisaschneider0509 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 lisaschneider0509 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MedGen_Kallisto
1 lisaschneider0509 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MergeColumns
Merge datasets by column.
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  MergeFCSDataFiles
Merge multiple FCS data files into a single FCS datasets; includes multimple subsampling options.
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  MergeHTSeqCounts
Merges HTSeq read count data files into one file
1 Marked as production tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
0.9 Marked as production tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.7 Beta release with added feature of cls file creation and sample renaming bhill@broadinstitute.org https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
0.6 Beta release with added feature of cls file creation and sample renaming bhill@broadinstitute.org Installed from zip
  MergeRows
Merge datasets by row.
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  mesenchymal
describe it here
1 0 shamaineho Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  mesenchymal.pre
describe it here
1 0 carrano.anna@mayo.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MetageneProjection
Projects one or more data sets onto the metagene representation of another data set
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  MethylationCNVAnalysis
Methylation array preprocessing with the minfi R package and copy-number variation analysis with the conumee R package. Compatible with both 450k or EPIC array data.
4 Switch defaults to datasets from gpftp ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Switch defaults to datasets from gpftp ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.4 geneslist optional edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
2.3 Controls can also be EPIC 2019. chapmano A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.2 Update for EPIC 2019. edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1.0.0 ckmah Installed from zip
  Microarray
3 tacazares Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 tacazares Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 tacazares Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  mihriban
describe it here
1 0 aydogan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  mihriban
describe it here
2 0 aydogan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 aydogan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  mihriban
describe it here
1 0 aydogan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MINDY
Runs the MINDY algorithm for inferring genes that modulate the activity of a transcription factor at post-transcriptional levels
2 Fixed parsing of optional parameter dpi transcription factor list on command line pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  MINDYViewer
Visualizes the results of MINDY
1 Visualizes the results of MINDY pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  mirna.analysis
describe it here
2 0 kpagacz Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 kpagacz Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  monse
describe it here
1 0 monser9610 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  monse
describe it here
1 0 monser9610 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  monse
describe it here
1 0 monser9610 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MouseLiver
1 yiwenh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MouseLiver
1 yiwenh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MS_gene.enrichment
1 Jinxi Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  multi.gsea
3 stonilee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 stonilee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 stonilee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Multiple.ssGSEA
3 thk1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 thk1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 thk1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Multiple_ssGSEA_ROC
Simple_ssGSEA_ROC
11 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
10 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
9 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
8 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
7 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Multiple_ssGSEA_ROC
3 thk1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 thk1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 thk1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MultiplotStudio
Scatterplot visualization tool for analyzing differential gene expression.
1.5.62 Completely rewritten and vastly improved replacement for Multiplot bhill@broadinstitute.org Installed from zip
  MutPanning
MutPanning identifies driver genes based on their abundance of nonsynonymous mutations and their increased number of mutations in unusual nucleotide contexts that deviate from the background mutational process.
2 Initial Release bhill@broadinstitute.org Installed from zip
  MutSig
1 SwethaRaj Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MutSig_01
describe it here
2 0 lilianboll Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 lilianboll Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  mutsig_lt1
mutsig
1 gracejoo@skku.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  mutsig_ref
1 gracejoo@skku.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MutSigCV
Identifies genes that are significantly mutated in cancer genomes, using a model with mutational covariates.
1.3 Moved gp_MutSigCV executable into the 'genepattern/docker-mutsigcv:0.2' docker image pcarr@broadinstitute.org https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
1.3.5 updated taskType bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.3.4 Copied gp_MutSigCV to docker image pcarr@broadinstitute.org Installed from zip
1.2 Remove python dependency, use 'Matlab-2013a-MCR' environment and directly invoke the gp_MutSigCV executable pcarr@broadinstitute.org https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
  my.bowite.indexer
describe it here
2 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MycMut_Exp
1 lysis_2_kill Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
Identify differentially expressed genes
2 0 ValentinaJG Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 ValentinaJG Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
Identify differentially expressed genes
4 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
identify differentially expressed genes
3 amirferry Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 amirferry Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 amirferry Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
Identify differentially expressed genes
3 amirferry Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 amirferry Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 amirferry Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
describe it here
4 Mgrinwald Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 Mgrinwald Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 Mgrinwald Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Mgrinwald Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
describe it here
3 christoftaxis Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 christoftaxis Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 christoftaxis Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
identify differentially expressed genes
4 Lucas Huang Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 Lucas Huang Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 Lucas Huang Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Lucas Huang Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
ID differentially expressed genes
1 saipra003@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
describe it here
3 firoz Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 firoz Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 firoz Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
Identify differentially expressed genes
4 ch211493 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 ch211493 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 ch211493 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 ch211493 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Mycomparativemarkerselection
describe it here
2 0 acelyaavci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 acelyaavci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  mycomparativemarkerselection
describe it here
2 0 acelyaavci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 acelyaavci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
Identify differential gene expression
3 0 jacquelinemartin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 jacquelinemartin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 jacquelinemartin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
describe it here
1 0 jacquelinemartin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
DEG aml
4 sdeota Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 sdeota Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 sdeota Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 sdeota Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
describe it here
6 rnm53 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 rnm53 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 rnm53 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 rnm53 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 rnm53 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 rnm53 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
describe it here
2 0 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
expressed gene
4 nayoung828 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 nayoung828 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 nayoung828 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 nayoung828 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComparativeMarkerSelection
identify differentially expressed genes
3 0 ssridhar Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 ssridhar Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 ssridhar Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyCompartiveMarkerSelection
Identify differentially expressed genes
4 jacquelinemartin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 jacquelinemartin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 jacquelinemartin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 jacquelinemartin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyCompartiveMarkerSelection
identifying differentially expressed genes
3 khalil.z Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 khalil.z Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 khalil.z Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyComprativeMarkerSelection
Identify differentially expressed genes
6 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyogenicDifferentiation
1 busrayi Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  MyPipelien
describe it here
1 0 firoz Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  myPipeline
1 fravitali Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  mzXMLToCsv
Converts a mzXML file to a zip of csv files
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  N22
describe it here
1 0 ymavura Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  NanoStringNormalizer
1 ecrouchet@unistra.fr Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  NearestTemplatePrediction
Nearest neighbor prediction based on a list of marker genes
6 Updated to use R-3.1 and added HTML documentation. ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4 Updated to use R-3.1 and added HTML documentation. pcarr@broadinstitute.org A GenePattern module repository whose content is contributed by members of the GenePattern community. These modules are not curated by the GenePattern team. GParc (GenePattern Archive)
  NivoTad.Supervised.GSEA
1 Jefferson Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  NMF
describe it here
1 0 monser9610 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  NMF
Non-negative Matrix Factorization
2 Annotated for GP 1.4 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.1 Annotated for GP 1.4 tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  NMFClustering
GPU-backed implementation of non-negative Matrix Factorization (NMF) Consensus Clustering.
7 Using mini-batch k-means for clustering ted Installed from zip
  NMFConsensus
Non-negative Matrix Factorization (NMF) Consensus Clustering
5 Added output files to manifest. Doc edits. pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  no1
describe it here
1 0 amaretto-team Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  No_exo_1_R1.fastq.gz
describe it here
1 0 thepreztonlee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Normalizacin
describe it here
1 0 nashe_li Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Normalization.Nanostring
2 nevena.slovic@etu.unistra.fr Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 nevena.slovic@etu.unistra.fr Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  normalizeRNAseq
2 edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  nur.demirci
describe it here
1 0 nurdemirci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Nur.DEMRC
describe it here
2 0 nurdemirci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 nurdemirci Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  One
describe it here
2 0 Amrutesh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Amrutesh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  oo
describe it here
1 0 wklove Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  oooo
describe it here
1 0 SENTHIL Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  OpenCRAVAT
<img src="https://opencravat.org/images/OpenCRAVAT_Logo-0-sm.png" width=50px alt="img"/>OpenCRAVAT performs genomic variant interpretation including variant impact, annotation, and scoring.
1 inital release bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.3 inital release ted Installed from zip
1.1 inital release ted Installed from zip
  OutSplice
OutSplice is a package that compares alternative splicing events between tumor and normal samples. This package is specifically designed for analyzing the gene and junction information from RNA sequencing data provided by the user, or from the TCGA. This package generates a matrix of splicing outliers, which are junctions that are either significantly over or under-expressed compared to a control sample. OutSplice further designates observed outliers as skipping, insertion, or deletion events. Overall, OutSplice is novel in that it determines differential splicing burdens between tumors and normal samples and characterizes the nature of splicing outliers.
3 Remove genome, txdb and annotation parameters, leaving only the presets ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Remove genome, txdb and annotation parameters, leaving only the presets ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Remove genome, txdb and annotation parameters, leaving only the presets ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  OutSplice.plotJunctions
Using the result file from OutSplice, OutSplice.plotJunctions creates bar and waterfall plots of junction expression in both the tumor and normal samples.
3 Initial Revision. ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Initial Revision. ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Initial Revision. ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Ovarian_EMT
describe it here
14 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
13 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
13.3 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
13.2 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
13.2.3 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
13.2.2 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
13.2.1 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
13.1 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
12 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
11 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
10 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
9 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
8 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
7 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PAAD_CNV
1 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PAAD_CNV1
2 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PCA
Principal Component Analysis (adapted from MeV, http://www.tm4.org/m)
4 Updated documentation pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4.2 Updated documentation eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4.1 Updated documentation eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  pca
describe it here
1 0 trandoanduyhai Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PCAViewer
Principal Component Analysis Visualizer (adapted from MeV, http://www.tigr.org/software/tm4/mev.html)
6 Fixed bug with 3D plot with legend not properly saved on non-Windows machines pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  PclToGct
Convert Stanford preclustering file (.pcl) to .gct
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  PCNSL_MutSigCV
2 xeyu17@fudan.edu.cn Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 xeyu17@fudan.edu.cn Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PD1
1 studyong Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PD2
1 studyong Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PDL1lung
1 studyong Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Peaks
Determine peaks in the spectrum using a series of digital filters.
2 Updated for R 2.5 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  philip
describe it here
2 0 landa Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 landa Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Picard.AddOrReplaceReadGroups
Replaces all read groups in the input file with a new read group and assigns all reads to this read group in the output
3 Read Group ID is now a required Parameter. pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Picard.BamToSam
Converts a BAM file to a SAM file
2 Renamed from BamToSam to Picard.BamToSam pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Picard.CreateSequenceDictionary
Reads FASTA or FASTA.GZ files containing reference sequences, and writes them as a SAM file containing a sequence dictionary
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Picard.FastqToSam
Extracts read sequences and qualities from the input fastq file and writes them into the output file in unaligned SAM or BAM format
2 Renamed from FastqToSam to Picard.FastqToSam pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Picard.MarkDuplicates
Examines aligned records in the supplied SAM or BAM file to locate duplicate reads.
2 Added sorting collection size ratio parameter and modified to print warning message about failed file delete attempts to stdout pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Picard.ReorderSam
Reorders a SAM file or a BAM file to match contig ordering in a provided reference file
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Picard.SamToBam
Converts a SAM file to a BAM file
2 Renamed from SamToBam to Picard.SamToBam pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Picard.SamToFastq
Convert SAM or BAM files to FASTQ format
3 Fixed issue with choice parameters not appearing as drop downs pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Picard.SortSam
Sorts a SAM or BAM file in a specified order
4 Renamed from SortSam to Picard.SortSam pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  pip
1 Angelica461 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  pip
describe it here
1 0 applehur Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PIPE1
1 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipe_MutSigCV
1 sguib Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline
describe it here
1 0 aster1217@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline
describe it here
2 0 yuduoduo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 yuduoduo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PIPELINE
describe it here
1 0 monser9610 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline
describe it here
1 0 Nour1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline
1 sevvaldik Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline
describe it here
1 0 Nour1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.0421
describe it here
1 0 keina.0328@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.0522
describe it here
1 0 keina.0328@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.07112020
4 mauro campanella Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 mauro campanella Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 mauro campanella Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 mauro campanella Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1
describe it here
1 0 ValentinaJG Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1
describe it here
1 0 Abrilmercado Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1
describe it here
1 0 khushbhullar Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1
describe it here
1 0 ivanz@vin.bg.ac.rs Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1
describe it here
1 0 MoonSun Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1
describe it here
1 0 kuelp Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1
describe it here
1 0 ychmax8@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1
describe it here
1 0 Shakira Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1.comparative.marker.selection.
describe it here
2 0 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1.kmeansclustering
describe it here
2 0 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.11
describe it here
1 0 YuanLin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.11
describe it here
1 0 Drhai Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.123
describe it here
1 0 b1951951 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.1st
describe it here
1 0 jooyong0308@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.2
describe it here
1 0 lbaert Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.2
describe it here
1 0 mahaitao18580092262 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.2.comparative.marker.selection
identify DE genes
5 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.2.kmeansclustering.
describe it here
3 0 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 kathyhan98 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.20190712DNM2RNAseq
1 yaling.wu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.2D3D.compare
2 cjk31714 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 cjk31714 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.33
describe it here
1 0 apacis Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.4
describe it here
1 0 dolphin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.48sample_chishao
1 Daisy Dai Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.55
describe it here
1 0 yitao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.72h_znf
1 lysk3490 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.88
describe it here
1 0 jessie61886@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.92.1.FR92.1.DMSO.Onken
describe it here
1 0 eanderson34 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.all_thresholded.by_genes.txt.
describe it here
2 0 guest_96206 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 guest_96206 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.for.QC.and.normalisation.of.EMEXP3583
1 Shakira Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.MyComparativeMarkerSelection
Identify differentially expressed genes
3 ch211493 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 ch211493 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 ch211493 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline.MyComparativeMarkerSelection
identify differentially expressed genes
4 s6swchan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 s6swchan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 s6swchan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 s6swchan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  pipeline.tutorial
describe it here
1 0 zhanglim3 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  pipeline_eserc
1 Alberto_Gualtieri_1993 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  pipeline_rep
describe it here
3 0 sciencekey Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 sciencekey Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 sciencekey Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Pipeline_test_EM
RNA Seq 2 groups
1 v1 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PipelineKNN_test
1 alsawao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  pipline_esercitazione
1 Alberto_Gualtieri_1993 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PippaLine
1 isaia Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  plot
describe it here
1 0 lisdasuteja Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PlotPeaks
Plot peaks
2 Updated for R 2.5 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  PlvCtrl6308
1 singhuh00 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PNGNMFConsensus
Non-negative Matrix Factorization (NMF) Consensus Clustering
2 convert pdf to png ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Added output files to manifest. Doc edits. ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  polyau_preleuk_ssgsea_test
describe it here
1 0 samuel1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  polyau_ssgsea_viz_testing
describe it here
1 0 samuel1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  pp
describe it here
1 0 coco06 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  pptm
describe it here
1 0 jgriffin567 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  practice1
describe it here
1 0 kedar Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PredictionResultsViewer
Visualizes prediction results in JavaScript
4.11 Bug fix for S3 files tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4.10 JavaScript implementation of PredictionResultsViewer bhill@broadinstitute.org https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
4.9 JavaScript implementation of PredictionResultsViewer bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Includes interactive plot of prediction results pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Preprocess_tutorial
1 alsawao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PreprocessDataset
Performs several preprocessing steps on a res, gct, or odf input file
5 convert over to html doc pcarr@broadinstitute.org Installed from zip
5.1 Bug fix for optional 'threshold.for.removing.rows' and 'number.of.columns.above.threshold' module params ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Added additional filtering options pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  preprocessed.gct
describe it here
1 0 96Gerar Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PreprocessVelocityTranscriptome
Extract transcript and intron sequences from the genome sequence using the eisaR package in order to quantify both intronic (unprocessed) and exonic (processed) RNA abundances in each cell with alevin.<br>A necessary preprocessing step to enable RNA velocity analysis.
1 initial release bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  PreviewFCS
Allows viewing of structural metadata, parameters, and descriptive statistics from a Flow Cytometry Standard (FCS) data file
2 Fix for parsing empty keyword values pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  PrivateCloud
test of permissions
1 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  process
describe it here
2 0 HUANGSHUAI Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 HUANGSHUAI Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Processing
describe it here
1 0 smgxopk Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ProstateMRSamp1
1 trostels Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ProteoArray
LC-MS proteomic data processing module
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  proteoGSEA_Ant_Rome
1 ferjmnz Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ProteomicsAnalysis
Runs the proteomics analysis on the set of input spectra
2 Updated for R 2.5 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  prova
1 AngelicaR Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  prova
describe it here
1 0 AFALANGA Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Prova
describe it here
1 0 g.armani Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  prova
1 debora_dallera Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  prova.2
2 mauro campanella Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 mauro campanella Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Prova1
1 debora_dallera Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Prova1
6 Mattia_gp2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 Mattia_gp2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 Mattia_gp2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 Mattia_gp2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 Mattia_gp2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Mattia_gp2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Prova1
1 Giuseppe.serio01 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  prova_bioinformatica
1 valentina1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  prova_corso_bioinf_AT
3 Alicesalvadeo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 Alicesalvadeo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Alicesalvadeo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  prova_corsoBioinformatica
2 Mattia_gp2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Mattia_gp2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PTM_SEA
PTM-SEA for use with PTMsigDB
4 Initial Version to accompany PTM-SEA manuscript pcarr@broadinstitute.org Installed from zip
2 0 pcarr@broadinstitute.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 pcarr@broadinstitute.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PTMSEA.Pipeline.FMA
1 fahsan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PTMSEA.try
describe it here
1 0 gramirez Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  pvec.paper
1 fkipper Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  pvec_npc.vs.pvec
describe it here
1 0 fkipper Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  PyCoGAPS
Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis. This package, PyCoGAPS, presents a unified Python interface, with a parallel, efficient underlying implementation.
4 Updated parameter descriptions for max gibbs A and P ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Updated parameter descriptions for max gibbs A and P ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Updated parameter descriptions for max gibbs A and P ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Updated parameter descriptions for max gibbs A and P ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  q
describe it here
1 0 MartaRojas Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  qPCR_heatmap_secscreen
1 cbudjan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  qupathtofcsPipeline
qupath
1 gabrielascui Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  r
describe it here
1 0 kimmcl860 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  raanvi
describe it here
1 0 raanvi Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ran.seq
3 bioraghu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 bioraghu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 bioraghu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RandomForest
Performs random forest classification on data and class files (cross-validation or test-train prediction), outputting a prediction results file.
4 Module filename bug fixes edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Version 2, includes confidence scores, feature importance, and model in/output edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Initial beta version (equivalent to Dev 1.0) edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  RankNormalize
Normalize the rows in a data set by rank
1.10 Updated to make use of the R package installer and add HTML documentation. edwin5588 A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  Read_group_trackingToGct
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Converts a Cufflinks read_group_tracking file into GCT format
0.15 Updated to accept a mapping file to convert tracking IDs to gene names. pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  reg
describe it here
1 0 Rezwan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  REMBRANDT.pipeline
3 svdvoort Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 svdvoort Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 svdvoort Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RemoveMissingValues
Removes features and/or samples containing missing (NA) values
1 Public Release pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  RemoveSaturatedFCSEvents
Remove saturated events from an FCS data file
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  RenameFile
Creates a result file with the contents of the input but with a new name. Where possible, this is done without copying the file but instead by simply making a link. While it is possible to run this with a submitted file, the common use will be to change the name of a result file or a previously uploaded file. Note that the original file will still be present in its original location.
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ReorderByClass
Reorder the samples in an expression dataset and class file by class
3 Fixed default value for class file output name pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  report
describe it here
1 0 aru2001 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  results
describe it here
1 0 sdh1621 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  rf
describe it here
1 0 ameetmishra Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNA.Prdm12
1 tkokotovic Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNA.seq.analysis.test.2.tuxedo_new
1 jdyee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  rna.seq.KI.vs.WT
1 bioraghu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNA_EX
2 osamasweef Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 osamasweef Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNA_exp
1 jmargari Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNA_exp
1 Takeshi Masuda Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNA_exp
1 jbzhang Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNA_seq
3 byuen_pactpharma Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 byuen_pactpharma Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 byuen_pactpharma Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNA_seq
1 seisen27 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNA_Seq
1 seisen27 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  rna_seq
3 scientistbill Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 scientistbill Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 scientistbill Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAExp
1 aximinies Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAexp_PVL20200402
RNA seq pipeline for bulk rna
1 desai.krisha Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseq
1 wmr23 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  rnaseq
describe it here
2 0 ddaizi Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 ddaizi Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseq
1 xiaohua Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  rnaseq
describe it here
4 0 mmurugesan@coh.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 0 mmurugesan@coh.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 mmurugesan@coh.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 mmurugesan@coh.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseq
1 jbzhang Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNASeq
5 VeraK Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 VeraK Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 VeraK Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 VeraK Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 VeraK Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseq.analysis.test.run
1 jdyee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseq.GSEA
1 pem20bf Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseq.pipeline.v1
3 userlee7655-2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 userlee7655-2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 userlee7655-2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseq.sms4
1 Samii8 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNASeq.TCGA
1 jsussman Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseq_corso_bioinf
2 Matteo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Matteo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseq_DESeq2
RNA seq DESeq2
12 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
11 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
10 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
9 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
8 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
7 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1.1 v1 etienne.moussay@lih.lu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseq_exp
1 xiaohua Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNAseqc
3 bgfritz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 bgfritz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 bgfritz1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  RNASeQC
Calculates metrics on aligned RNA-seq data.
2 Renamed from RNAseqMetrics pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2.15 Beta Release: Updated with RNASeQC.jar build 8.7.13. Currently outputs INFO and WARNING to stdout pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  rtgg
describe it here
1 0 JavierRobles272 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SageKda2Cys
Takes a zip of KeyDriverAnalysis output files and formats them as a cytoscape .cys session file
6 tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  Salmon.Alevin.Quant
Quantification and analysis of 3' tagged-end single-cell sequencing data using Salmon's Alevin (v1.5.2) function.<br> See: <a href="https://salmon.readthedocs.io/en/latest/alevin.html" target="_blank">The Alevin Documentation</a> for detailed usage guidelines.
0.6 Alevin 1.5.2 - beta release bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Salmon.Indexer
Salmon (version 1.6.0) transcriptome indexer.<br> See: <a href="https://salmon.readthedocs.io/en/latest/salmon.html#using-salmon" target="_blank">The Salmon User Guide</a> for detailed usage guidelines.
0.5 Updated to Salmon 1.6.0 and added support for transcriptome only index bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Salmon.Quant
Perform transcript-level quantification of RNA-seq data using Salmon (version 1.6.0).<br> See: <a href="https://salmon.readthedocs.io/en/latest/salmon.html#using-salmon" target="_blank">The Salmon User Guide</a> for detailed usage guidelines.
0.9 Update to Salmon v1.6.0 and add Gencode Human release v39 and Mouse release vM28- beta update bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  sample_combat_results
describe it here
1 0 ncastano Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SamTools.FastaIndex
Indexes a reference sequence in the FASTA format
0.3 Improved error message for different line length in sequence error tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  ScanpyQC
Create Scanpy Quality Control Plots to enable unblinded dataset filtering with ScanpyUtilities
2 first Jenkins prerelease acastanza A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 first Jenkins prerelease ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ScanpyUtilities
Scanpy preprocessing of an h5 single cell RNASeq dataset
1 Updated h5ad version and added mitochondrial filtering support on 10/04/2021 ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.3 Updated h5ad version and added mitochondrial filtering support on 10/04/2021 tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.8 Working revision from Gevaert lab git repo on 10/16/18 ted Installed from zip
0.7 Working revision from Gevaert lab git repo on 10/16/18 ted Installed from zip
0.06 Working revision from Gevaert lab git repo on 10/16/18 ted Installed from zip
0.05 Working revision from Gevaert lab git repo on 10/16/18 ted Installed from zip
0.04 Working revision from Gevaert lab git repo on 10/16/18 ted Installed from zip
0.03 Working revision from Gevaert lab git repo on 10/16/18 ted Installed from zip
0.2 Working revision from Gevaert lab git repo on 10/16/18 ted Installed from zip
0.02 Working revision from Gevaert lab git repo on 10/16/18 ted Installed from zip
  scVelo
Module for performing basic velocity analysis using the scVelo protocol on ScanpyUtilities processed datasets
2 Initial release tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Initial release bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  sec.clones
describe it here
1 0 kamyar Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SelectFeaturesColumns
Takes a 'column slice' from a .res, .gct, .snp, .cn, .loh, .odf, or .cls file.
4 Added support for .snp, .cn, and .loh files pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Added cls file input option and updated task description pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SelectFeaturesRows
Generate a .res, .gct, .snp, .cn, .loh, or .odf file containing only specified features (i.e. rows).
4 Added support for .snp, .cn, and .loh files pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SelectFileMatrix
A helper module which selects a matrix out of a delimited text file.
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  selectingGenes_329
1 lydia.lam Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SelectSNPProbes
Filter to keep just copy number probes
0.4 Modified to append extension of input file to output file and input and output file formats and added doc tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  SetFCSKeywords
Sets keyword/value(s) in a Flow Cytometry Standard (FCS) file.
2 Fix for parsing empty keyword values pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  seurat
describe it here
2 0 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Seurat.BuffetPreprocessing
Seurat preprocessing
2 display seurat object sizes jonzamora Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Editing parameter groups jonzamora Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Seurat.Clustering
Companion module for the <a href="https://notebook.genepattern.org/services/sharing/notebooks/376/preview/">Seurat notebook</a>. Performs clustering and marker identification on single cell data.
1.2 Updating to run Seurat 4.0.3 edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1.1 Updating to run Seurat 4.0.3 edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.6 Adding link to notebeook + patching a parameter so it reflects the actual options. edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.5 Adding number of cluster markers as option + fixed docker container. edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.3 Adding number of cluster markers as option. edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.2 Updating module description. edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  Seurat.DietPreprocessing
Seurat Preprocessing
1 Include new parameter for Diet Seurat Preprocessing jonzamora Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Seurat.IntegrateData
Batch Correction for Seurat Objects
1.3 Upgrading to Seurat V4 and fixing a bug in the command line and file name edjuaro Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Seurat.IntegrateData
Batch Correction for Seurat Objects
4.1 Upgrading to Seurat V4 and fixing a bug in the command line and file name tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  Seurat.Preprocessing
Seurat preprocessing
4 Upgrading to Seurat 4.0.3 edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4.1 Upgrading to Seurat 4.0.3 edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
3 Editing parameter groups jonzamora Installed from zip
3.2 Upgrading to Seurat 4.0.3 edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
3.1 Upgrading to Seurat 4.0.3 edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1 Editing parameter groups edjuaro Installed from zip
1.1 Upgrading to Seurat v4.0.3 edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.12 Reading the RDS file edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.11 Reading the RDS file edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.10 Reading the RDS file edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.9 Parsing zip files v3 edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  Seurat.PreprocessingNullFeatures
Seurat preprocessing
1 Upgrading to Seurat 4.0.3 jonzamora Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Seurat.QC
Seurat quality control (First step in the Seurat Suite), using Seurat version 4.0.3.
4 Reading new version of HCA (Loom) edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4.11 Reading new version of HCA (Loom), fixing the url reading bug (added a new parameter) edjuaro Installed from zip
3.3 Reading new version of HCA (Loom) edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
3.1 Making the creation of the TXT file optional. jonzamora Installed from zip
2 Renaming some parameters edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
0.16 Renaming some parameters edjuaro A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  Seurat.VisualizeMarkerExpression
Visualize Marker Expression as violin plots and on a UMap. To be used after Seurat.Clustering
2 Same as first version, oficial release. edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 First version edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  seuratclustertestedw
Companion module for the <a href="https://notebook.genepattern.org/services/sharing/notebooks/376/preview/">Seurat notebook</a>. Performs clustering and marker identification on single cell data.
2 Updating to run Seurat 4.0.3 edwin5588 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 Updating to run Seurat 4.0.3 edwin5588 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  sfs
describe it here
2 0 liuzaoqu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 liuzaoqu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  shRNAscores
Outputs fold change, signal to noise and modified score (which deweights highly variable hps from reference control) for RNAI HP scoring
0.4 changed name of module tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  signatures
describe it here
1 0 tlobo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Simple_ssGSEA_and_ROC_curve
1 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  skcm.clustering
skcm clustering
3 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 eshelden Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SKCM2
describe it here
1 0 rohits Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SKCMConCluFPKMUQ_12052018
1 lydia.lam Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SKCMConsensusCluster_12032018
1 lydia.lam Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SKCMConsensusClusterFPKMUQ_12042018
1 lydia.lam Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SLE_Data
2 sc9295 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 sc9295 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  sleep
just take some time and write a file
3 ted Installed from zip
  snp
describe it here
1 0 dinayamin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SNP.Copy.Number.and.Loss.of.Heterozygosity.Estimation
6 Niktdak Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 Niktdak Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 Niktdak Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 Niktdak Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 Niktdak Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SNPFileCreator
Performs normalization and probe-level summarization to generate a SNP file for a set of Affymetrix SNP chip CEL files.
3.12 Modified to output only snp format tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SNPFileCreator_1chip
Processes Affymetrix SNP probe-level data into expression values
0.3 tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  SNPFileCreator_SNP6
Performs normalization and probe-level summarization to generate a SNP file for a set of Affymetrix SNP chip CEL files.
1.2 Updated doc to html tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  SNPFileSorter
Sorts a .snp file by Chromosome and location
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SNPMultipleSampleAnalysis
Determine Regions of Concordant Copy Number Aberrations
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.3 changed cytoband to <libdir>CytoBands.txt - per Josh's suggestion in gpat-189 tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  SnpViewer
Displays a heat map of snp data
3 Fixes bug with legend thresholds pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SOMClustering
Self-Organizing Maps algorithm
2 Updated to latest file parsers and annotated for GP 1.4 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SOMClusterViewer
Visualize clusters created with the SOM algorithm
5 Fixes redraw bug pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
5.1 Added ability to scroll the left panel pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  sortSam
1 bb3029@cumc.columbia.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SPARCS
1 sheilazt Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SparseHierarchicalClustering
Cluster the samples in a data matrix using an adaptively-chosen subset of the features.
1 Public Release pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.1 Public Release tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  spatialGE.Preprocessing
The package spatialGE provides a collection of tools for the visualization of gene expression from spatially-resolved transcriptomic experiments. The data input methods have been designed so that any data can be analyzed as long as it contains gene expression counts per region of interest (ROI), spot, or cell, and the spatial coordinates of those ROIs, spots, or cells, as it is generated in platforms such as GeoMx, Visium, and CosMx-SMI. The spatialge.Preprocessing module performs initial data ingestion, filtering, transform and pseudo-bulk operations to prepare data for further processing. Order of operations are: ingestion, filter, pseudobulk, transform.
5 Strip .tar from output filenames if its part of the input filename. Stop putting .rds on the rds file twice. ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4 Updated to use GitHub Pages doc url rather than doc.html ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Updated to use GitHub Pages doc url rather than doc.html ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Updated to use GitHub Pages doc url rather than doc.html ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  spatialGE.SpatialAutocorrelation
This function performs spatial statistics analysis on spatial transcriptomics data using the SThet module.
1 ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  spatialGE.STclust
This function performs spatial clustering on gene expression data using the STclust method.
1 edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  spatialGE.STenrich
Detect genes showing spatial expression patterns (e.g., hotspots). Tests if spots/cells with high average expression of a gene set shows evidence of spatial aggregation.
1 Initial development release tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SplitColumns
Creates a separate file for each column specified from the input file
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SplitDatasetTrainTest
Splits a dataset (and cls file) into a number of train and test subsets
4 Added output types train.0.gct, test.0.gct, train.1.gct, test.1.gct, et cetera pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ssGESA
1 georgewu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGESEA
describe it here
1 0 Kkkkate Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssgsea
1 christophe.goncalve@mail.mcgill.ca Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA
1 effe_li Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA
Performs single sample GSEA. NOTE: with the release of v10.0.1, this module was renamed from "ssGSEAProjection" to just "ssGSEA"
10.1.0 10/03/2022 : Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10.0.12 09/15/2022 : Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10.0.11 01/19/2022 : Updated to MSigDB v7.5.1. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10.0.10 01/12/2022 : Updated to MSigDB v7.5. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10.0.9 04/22/2021 : Fixed minor typo. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10.0.8 04/01/2021 : Updated for MSigDB v7.4. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10.0.7 03/22/2021 : Updated for MSigDB v7.3. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10.0.6 12/16/2020 : Fix for single sample GCT files and single set GMX files. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10.0.4 09/23/2020 : Updated to MSigDB v7.2. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10.0.3 04/02/2020 : Updated to MSigDB v7.1. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
10.0.2 03/10/2020 : Renamed from ssGSEAProjection. Updated to R-3.2. Documentation updates. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
9.1.2 Updated to give access to MSigDB v7.0. Unified the Gene Set DB selector parameters and better downloading of MSigDB files. Removed Java dependency. Updated to give access to MSigDB v7.0. Added a no-normalize option as the default. eby@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ssgsea
describe it here
1 0 ltinoue Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA.Analysis
describe it here
1 0 amassa Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA.Eide.dataset
2 hhalse Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 hhalse Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA.ROC
Generate ROC curves and calculate the AUC from ssGSEA results and a binary phenotype classification.
1 ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  ssGSEA.success
describe it here
1 0 ldzier Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA.to.ConstellationMap
describe it here
1 0 mverber1114 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA_1
1 mestrada Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA_20_SCLC
ssGSEA for 20 SCLC
1 MarcoMernberger Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA_allgenesets
5 samuel1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 samuel1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 samuel1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA_and_ROC_for_set_eight
3 thk1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 thk1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA_CCLE_v1
describe it here
1 0 mitsuishi.y Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA_JT
describe it here
1 0 sturcan1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA_Luca
1 lucaT Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA_prompt
2 MarcoMernberger Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 MarcoMernberger Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEA_test
describe it here
1 0 HauslerD Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssgsea_viz_testing
describe it here
1 0 samuel1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEAandROC
5 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 TaeHoon5314 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssGSEATest1
1 anicolau Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  ssgseaviewing
describe it here
1 0 guest_96395 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  STAD
describe it here
1 0 ZANGYue Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  STAR.aligner
STAR (Spliced Transcripts Alignment to a Reference) 2.7.10b is a fast RNA-seq reads to genome mapper. It differs from other mappers as TopHat in that it gains speed at the expense of consuming more RAM and that it incorporates transcriptome annotation at the indexing build stage rather than at the analysis stage. It can optionally detect non-canonical splices and chimeric transcripts.
2 Adding support for gzipped input data edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4 Update to STAR 2.7.10.b ted A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
1.3 Genome folder stubbed out until it can be hosted somewhere retrievable via http instead of ftp ted A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  star.alignment
describe it here
2 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 csusm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  STAR.indexer
The STAR indexer (version 2.7.10b) makes from a series of fastA files containing a genome an index for use with the STAR spliced read to genome aligner. It can optionally (but highly recommended !) incorporate information about known intron-exon junctions.
1 Rename index.dir parameter to output.file ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
0.50 Rename index.dir parameter to output.file ted A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.48 Update to STAR 2.7.10b ted A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.46 Update to STAR 2.7.1a ted A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  STREAM.DetectDifferentiallyExpressedGenes
Used to detect differentially expressed genes between pairs of branches.
0.12 inital revision ted Installed from zip
  STREAM.DetectLeafGenes
Detect marker genes for each leaf branch.
0.12 inital revision ted Installed from zip
  STREAM.DetectTransitionGenes
Detects the transition genes for each branch of a STREAM trajectory.
0.3 inital revision ted Installed from zip
  STREAM.DimensionReduction
Perform dimension reduction on the dataset to make it easier to reliably assess similarity or distances between cells. Starting from the genes selected in the STREAM.FeatureSelection module, we project cells to a lower dimensional space using a non-linear dimensionality reduction method.
0.7 inital revision tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.6 inital revision ted Installed from zip
0.5 inital revision ted Installed from zip
  STREAM.ElasticPrincipalGraph
STREAM (Single-cell Trajectories Reconstruction, Exploration And Mapping) is an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. STREAM.ElasticPrincipalGraph is uses elastic principal graph learning to calculate a pseudotime trajectory.
0.4 inital revision ted Installed from zip
  STREAM.EPGAdjustFinalGraph
Adjust the final EPG trajectory structure by pruning, extending and otherwise modifying the branches to optimize for single-cell data
0.6 inital revision ted Installed from zip
  STREAM.FeatureSelection
Select either or both of the most variable genes and then find the principal components using PCA. These will then be available for the downstram trajectory analysis.
0.6 inital revision ted Installed from zip
  STREAM.Plot2DVisualization
STREAM.Plot2DVisualization is used to check if there is clear meaningful trajectory pattern via TSNE or UMAP 2-D plots. If so, we can continue the STREAM analysis; If not, go back to previous steps (preprocessing, feature selection and dimension reduction) to modify the parameters.
0.15 inital revision ted Installed from zip
0.14 inital revision ted Installed from zip
  STREAM.Preprocess
Preprocess single cell RNA-seq data to prepare it for the STREAM trajectory analysis. This module will normalize, log transform, filter and remove mitochondiral genes.
0.4 inital revision ted Installed from zip
  STREAM.SeedEPGStructure
Seeding the initial elastic principal graph prior to starting the trajectory learning process.
0.4 inital revision ted Installed from zip
  STREAM.VisualizeTrajectories
Generates flat tree subway and stream plots that intuitively represents trajectories as linear segments on a 2D plane
0.16 inital revision ted Installed from zip
  SUBMAP
describe it here
1 0 D201981538 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  SubMap
Maps subclasses between two data sets
4 Changed default value for the p-value correction method parameter and fixed bug which occurs when there is one instance of a class ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3 Changed default value for the p-value correction method parameter and fixed bug which occurs when there is one instance of a class pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SurvivalCurve
Draws a survival curve based on a cls file
3 Modified to use R 2.7 and Cairo to output images in PNG format ted Installed from zip
2 added pdf survival curve output format pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SurvivalDifference
Tests for survival difference based on cls file
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  SVM
Classify samples using SVM
4 Compute confidence for prediction results. pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4.1 Added check that the user provided saved model is an SVM model tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  SysBio_HW1
5 ps1277 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 ps1277 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  T.cell.volcano.test
1 carmenyong Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Tangram
A method for spatial alignment of single cell transcriptomic data. See <a href=https://github.com/genepattern/Tangram/blob/main/README.md>documentation</a> for details on use cases.
5 Docker image update to v1.0 edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  TCGA.LIHC.beta.cat
describe it here
1 0 fahmida.rasha@utsouthwestern.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TCGA.LIHC.CTNNB1.step1
describe it here
2 0 fahmida.rasha@utsouthwestern.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 fahmida.rasha@utsouthwestern.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TCGA.SampleSelection
Retrieve TCGA data from Broad FireBrowse and perform sample selection on the basis of expression levels for specific genes of interest for analysis using GSEA tools.
3 Update for non-float MSigDB version numbers ted Installed from zip
2 Update for non-float MSigDB version numbers edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Update for non-float MSigDB version numbers edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
0.14 Update for non-float MSigDB version numbers bhill@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  TCGA.ssGSEA.ROC
Pipeline for ssGSEA_ROC analysis of TCGA samples
10 acastanza Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
9 acastanza Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
8 acastanza Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
7 acastanza Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 acastanza Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 acastanza Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TCGA.to.DESeq2
Retrieve count data from TCGA and run DESeq2 on it, also outputting normalized counts for GSEA and other tools
1 acastanza Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TCGA_BRCA
describe it here
1 0 l.chavez Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TCGA_THCA
1 haiyan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TCGABRCA
describe it here
1 0 Jasminetee Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TCGACNV
1 zhouguowei Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TCGAImporter
This module imports data from TCGA by taking in a GDC manifest file, downloading the files listed on that manifest, renaming them to be human-friendly, and compiling them into a GCT file to be computer-friendly.
6 Adding metadata to the docker container & updating to version 1.5 of the CLI. edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
5 Updating module to use the new docker container. edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
5.2 Bugfix: duplicated gene after translation. Also using new format in the command line on the manifest file. edjuaro https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
  TCGAImporter_test_pipelne
Download and collapse small dataset
3 1.0 edjuaro Installed from zip
  TedsAttackTest
A module for testing attacks against our server
999999999 ted Installed from zip
  test
describe it here
2 0 Della_123 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Della_123 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  test
describe it here
1 0 guest_97887 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Test.
1 Devansh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  test2
describe it here
1 0 Della_123 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  test3
describe it here
2 0 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 ted Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  tfsites.FindTfSitesAlteredBySequenceVariation
FindTfSitesAlteredBySequenceVariation reports the effects of all possible in silico single-nucleotide variants (SNVs) in a given sequence, for one transcription factor. Possible SNV effects include increasing (or optimizing) the affinity/score of a binding site, decreasing the affinity/score of a binding site, deleting a binding site, or creating a binding site.
1 Draft initial release ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  tfsites.GenerateMotifDatabase
GenerateMotifDatabase can be used to obtain position weight matrix (PWM) data to score binding sites in other TFSites modules. This tool extracts the PFM(s) for one or more transcription factor(s) of interest and then converts each PFM to its respective PWM.
1 Draft initial release ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  tfsites.NormalizeTfDNAAffinityData
NormalizeTfDnaAffinityData generates a relative affinity dataset which can then be used in other TFSites modules to score binding sites. This tool normalizes a raw affinity dataset relative to the sequence with the highest value that follows the core binding site definition. The resulting dataset will report the relative affinity value for every sequence in the original dataset, ranging from 0 to 1.
1 Draft initial release ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  tfsites.VisualizeTFSitesOnSequences
Annotates transcription factor binding sites across a DNA sequence. Multiple transcription factors can be analyzed. Each binding site is labeled with a unique binding site ID and its start and end position. If reference data is provided for a transcription factor, the affinity/score of this site will be labeled and the intensity of the binding site's color will be proporti
1 Draft initial release ted A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  TLS.signiture
1 sholmes.vs.jmoriarty@gmail.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TmapToGct
Converts a TMAP file to GCT format
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  tmp
describe it here
1 0 JieLan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  tracking.to.GCT
Seurat preprocessing
1 Parsing zip files marjanbrz Installed from zip
  Transcriptomics.Analysis
describe it here
1 0 cherkaos Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TransposeDataset
Transpose a Dataset - .res .gct, .odf
3 Added gct as an output format pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Trial
describe it here
1 0 ratna.wijaya Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Trial1
1 RebeccaAstley Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Trimmomatic
Provides a variety of options for trimming Illumina FASTQ files of adapter sequences and low-quality reads.
2 Replaced gpftp with datasets tabor A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1.4 updated convert phred scores value to preserve no convert option in pipelines pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  tryout
1 Himmel Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  TSGH.PM2.5.pathway.analysis
1 kunghsiuni Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  tst
tst
2 edwin5588 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 edwin5588 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Tutorial
describe it here
3 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 lalevesque95 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  tutorial.1
describe it here
3 0 Hoyaka Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 0 Hoyaka Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Hoyaka Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Tutorial.Pipeline
Generation of heat map of the expressed gene
2 0 Hoyaka Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 Hoyaka Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  tutorial01
1 renyow Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Tutorial_creating_a_workflow
describe it here
1 0 beaver9701 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  tximport.DESeq2
Imports RNA-seq quantifications from frequently used pipelines using the tximport package and outputs a DESeq2 "normalized counts" file in .GCT format suitable for use with GSEA, and/or a TPM .GCT suitable for ssGSEA.<br> If a Sample Info file is provided containing assignments of samples to phenotypes, gene level differential expression will be calculated using DESeq2 for the two phenotypes.
5 edwin5588 A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
4 acastanza A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3.8 ted A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
3.5 ted A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  txt2odf
This module turns a TXT file into an ODF file which can be used with other GenePattern Modules.
3 Cleaning up the release edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 First production release edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  txt2odf.20211130.colparams
This module turns a TXT file into an ODF file which can be used with other GenePattern Modules.THIS MODULE IS FOR USE IN THE Dec 21, 2021 workshop and is in active development
1.3 Making module public for workshop tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  UBE2D3TCGA.HCC
describe it here
1 0 HN Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UCEC
describe it here
1 0 Team_Julia Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UniquifyLabels
Makes row and column labels unique
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  UntitledPipeline1556
1 YWW Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline1950
1 guest_96467 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2016
1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2050
1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline211
1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2114
1 JinmingZhou Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2117
1 Jianfeng Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2134
1 lisafleischer1 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2166
1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2276
1 Devansh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2386
1 inga-maria.launonen@helsinki.fi Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2426
1 LilHasegawa Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2445
1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2477
1 Farahmandm Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2487
1 Mattia_gp2 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2498
1 caitlyn3@stanford.edu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2502
1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2505
1 jutjal Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2514
1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2568
1 wangyu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2568
1 wangyu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2568
1 wangyu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2568
1 wangyu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2568
1 wangyu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2575
1 aswani Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2614
1 jayantasthana Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2628
1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2638
1 qedos Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2667
1 huaixiaozi Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2702
1 YubinXie Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2748
1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2756
1 wangyu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2763
1 Belba112 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2806
2 actan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 actan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 rlunay Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 yiwenh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2828mouseliver
1 yiwenh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UntitledPipeline2831
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  UntitledPipeline2870
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1 hhyunji1027@naver.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 hhyunji1027@naver.com Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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  UntitledPipeline2925
1 YubinXie Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 YubinXie Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 YubinXie Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 rohitsingh Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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  UntitledPipeline3797
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  UntitledPipeline4393
ACC expression
1 rsirianni Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 Jinming Zhou Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 studyong Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 Wangjianwei Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 chuting Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 wangyu Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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s
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1 torch2sky Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 ymq Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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3 kdkorthauer Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 fravitali Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 liuhao Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 Kevin.Geistlich Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 Silvia Sabina Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 cmills2@fredhutch.org Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
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1 YWW Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  UploadFile
A utility for users to upload and share a common input file for use by modules within a pipeline.
0.1 tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  v1
describe it here
1 0 chanpulin Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Vaccinia.Affymetrix.Analysis.2020
7 jyothsnagirish Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
6 jyothsnagirish Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
5 jyothsnagirish Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
4 jyothsnagirish Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
3 jyothsnagirish Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
2 jyothsnagirish Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 jyothsnagirish Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Vaccinia.Affymetrix.Analysis.2020.v2
2 jyothsnagirish Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 jyothsnagirish Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  VennDiagram
Displays a Venn diagram
1 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  view
describe it here
1 0 nicolaco Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  viewer
describe it here
1 0 elenapip Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Visualizing.Filtered.DEGs
2 alow Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 alow Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1.2 alow Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1.1 alow Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  viz
describe it here
1 0 sophiespo Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  Voom.normalise.raw.counts.28921
describe it here
1 0 liana.gynn Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  VoomNormalize
Preprocess RNA-Seq count data in a GCT file so that it is suitable for use in GenePattern analyses. Formerly called "PreprocessReadCounts"
1.2 Creating anti-logged normalized values as one of the outputs & fixing documentation tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
0.9 Rename PreprocessReadCounts to VoomNormalize -- adding this to the description edjuaro A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
0.8 Rename PreprocessReadCounts to VoomNormalize edjuaro https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
0.7 set 'job.docker.image=genepattern/preprocessreadcounts'; containerize R packages pcarr@broadinstitute.org https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
0.6 pcarr@broadinstitute.org A GenePattern module repository containing beta releases of GenePattern modules. GenePattern beta
  WeightedVoting
Weighted Voting classification
3 Added additional feature selection options pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
1 Added java flag to allow this to run on unix servers lacking an X display pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  WeightedVotingXValidation
Weighted Voting classification with Leave-One-Out Cross-Validation
3 Added additional feature selection options pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
2 Correct ordering of class outputs, output class names in feature files, annotated for GP 1.4, updated file support libraries. pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
  Whole.exome.seq
1 1 silambarasan Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  WMr
1 wmr23 Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  WT_PD1
describe it here
2 0 ssarkar Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
1 0 ssarkar Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  wwy
describe it here
1 0 WWY Created on this server, as a clone of an existing module, or with the Module Integrator Created on server
  XChromosomeCorrect
Corrects X Chromosome SNP's for male samples.
3 pcarr@broadinstitute.org A repository of GenePattern modules curated by the GenePattern team. GenePattern production (new)
3.1 Fixed bug that required sample info file to have a Ploidy(numeric) column tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
  ZipFiles
Zips files
0.1 tabor A GenePattern module repository containing development quality releases of GenePattern modules. GenePattern dev
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